Using a structural and logics systems approach to infer bHLH–DNA binding specificity determinants
Numerous efforts are underway to determine gene regulatory networks that describe physical relationships between transcription factors (TFs) and their target DNA sequences. Members of paralogous TF families typically recognize similar DNA sequences. Knowledge of the molecular determinants of protein...
| Main Authors: | , , , , , , , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | en_US |
| Published: |
Oxford University Press (OUP)
2012
|
| Online Access: | http://hdl.handle.net/1721.1/70992 |
| _version_ | 1826205207962320896 |
|---|---|
| author | Masi, Federico De Grove, Christian A. Vedenko, Anastasia Alibes, Andreu Gisselbrecht, Stephen S. Serrano, Luis Walhout, Albertha J. M. Bulyk, Martha L. |
| author2 | Harvard University--MIT Division of Health Sciences and Technology |
| author_facet | Harvard University--MIT Division of Health Sciences and Technology Masi, Federico De Grove, Christian A. Vedenko, Anastasia Alibes, Andreu Gisselbrecht, Stephen S. Serrano, Luis Walhout, Albertha J. M. Bulyk, Martha L. |
| author_sort | Masi, Federico De |
| collection | MIT |
| description | Numerous efforts are underway to determine gene regulatory networks that describe physical relationships between transcription factors (TFs) and their target DNA sequences. Members of paralogous TF families typically recognize similar DNA sequences. Knowledge of the molecular determinants of protein–DNA recognition by paralogous TFs is of central importance for understanding how small differences in DNA specificities can dictate target gene selection. Previously, we determined the in vitro DNA binding specificities of 19 Caenorhabditis elegans basic helix-loop-helix (bHLH) dimers using protein binding microarrays. These TFs bind E-box (CANNTG) and E-box-like sequences. Here, we combine these data with logics, bHLH–DNA co-crystal structures and computational modeling to infer which bHLH monomer can interact with which CAN E-box half-site and we identify a critical residue in the protein that dictates this specificity. Validation experiments using mutant bHLH proteins provide support for our inferences. Our study provides insights into the mechanisms of DNA recognition by bHLH dimers as well as a blueprint for system-level studies of the DNA binding determinants of other TF families in different model organisms and humans. |
| first_indexed | 2024-09-23T13:09:05Z |
| format | Article |
| id | mit-1721.1/70992 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T13:09:05Z |
| publishDate | 2012 |
| publisher | Oxford University Press (OUP) |
| record_format | dspace |
| spelling | mit-1721.1/709922022-10-01T13:19:25Z Using a structural and logics systems approach to infer bHLH–DNA binding specificity determinants Masi, Federico De Grove, Christian A. Vedenko, Anastasia Alibes, Andreu Gisselbrecht, Stephen S. Serrano, Luis Walhout, Albertha J. M. Bulyk, Martha L. Harvard University--MIT Division of Health Sciences and Technology Bulyk, Martha L. Bulyk, Martha L. Numerous efforts are underway to determine gene regulatory networks that describe physical relationships between transcription factors (TFs) and their target DNA sequences. Members of paralogous TF families typically recognize similar DNA sequences. Knowledge of the molecular determinants of protein–DNA recognition by paralogous TFs is of central importance for understanding how small differences in DNA specificities can dictate target gene selection. Previously, we determined the in vitro DNA binding specificities of 19 Caenorhabditis elegans basic helix-loop-helix (bHLH) dimers using protein binding microarrays. These TFs bind E-box (CANNTG) and E-box-like sequences. Here, we combine these data with logics, bHLH–DNA co-crystal structures and computational modeling to infer which bHLH monomer can interact with which CAN E-box half-site and we identify a critical residue in the protein that dictates this specificity. Validation experiments using mutant bHLH proteins provide support for our inferences. Our study provides insights into the mechanisms of DNA recognition by bHLH dimers as well as a blueprint for system-level studies of the DNA binding determinants of other TF families in different model organisms and humans. National Institute of General Medical Sciences (U.S.) (DK068429) National Institute of General Medical Sciences (U.S.) (HG003985) European Union (PROSPECTS HEALTH-F4-2008-201648) 2012-06-01T18:28:46Z 2012-06-01T18:28:46Z 2011-02 2011-01 Article http://purl.org/eprint/type/JournalArticle 0305-1048 1362-4962 http://hdl.handle.net/1721.1/70992 De Masi, F. et al. “Using a Structural and Logics Systems Approach to Infer bHLH-DNA Binding Specificity Determinants.” Nucleic Acids Research 39.11 (2011): 4553–4563. Web. 1 June 2012. en_US http://dx.doi.org/10.1093/nar/gkr070 Nucleic Acids Research Creative Commons Attribution Non-Commercial http://creativecommons.org/licenses/by-nc/2.5 application/pdf Oxford University Press (OUP) Oxford |
| spellingShingle | Masi, Federico De Grove, Christian A. Vedenko, Anastasia Alibes, Andreu Gisselbrecht, Stephen S. Serrano, Luis Walhout, Albertha J. M. Bulyk, Martha L. Using a structural and logics systems approach to infer bHLH–DNA binding specificity determinants |
| title | Using a structural and logics systems approach to infer bHLH–DNA binding specificity determinants |
| title_full | Using a structural and logics systems approach to infer bHLH–DNA binding specificity determinants |
| title_fullStr | Using a structural and logics systems approach to infer bHLH–DNA binding specificity determinants |
| title_full_unstemmed | Using a structural and logics systems approach to infer bHLH–DNA binding specificity determinants |
| title_short | Using a structural and logics systems approach to infer bHLH–DNA binding specificity determinants |
| title_sort | using a structural and logics systems approach to infer bhlh dna binding specificity determinants |
| url | http://hdl.handle.net/1721.1/70992 |
| work_keys_str_mv | AT masifedericode usingastructuralandlogicssystemsapproachtoinferbhlhdnabindingspecificitydeterminants AT grovechristiana usingastructuralandlogicssystemsapproachtoinferbhlhdnabindingspecificitydeterminants AT vedenkoanastasia usingastructuralandlogicssystemsapproachtoinferbhlhdnabindingspecificitydeterminants AT alibesandreu usingastructuralandlogicssystemsapproachtoinferbhlhdnabindingspecificitydeterminants AT gisselbrechtstephens usingastructuralandlogicssystemsapproachtoinferbhlhdnabindingspecificitydeterminants AT serranoluis usingastructuralandlogicssystemsapproachtoinferbhlhdnabindingspecificitydeterminants AT walhoutalberthajm usingastructuralandlogicssystemsapproachtoinferbhlhdnabindingspecificitydeterminants AT bulykmarthal usingastructuralandlogicssystemsapproachtoinferbhlhdnabindingspecificitydeterminants |